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Abdelaal MR, Ibrahim E, Elnagar MR, Soror SH, Haffez H. Augmented Therapeutic Potential of EC-Synthetic Retinoids in Caco-2 Cancer Cells Using an In Vitro Approach. Int J Mol Sci 2022; 23:ijms23169442. [PMID: 36012706 PMCID: PMC9409216 DOI: 10.3390/ijms23169442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 07/29/2022] [Accepted: 08/05/2022] [Indexed: 11/16/2022] Open
Abstract
Colorectal cancer therapies have produced promising clinical responses, but tumor cells rapidly develop resistance to these drugs. It has been previously shown that EC19 and EC23, two EC-synthetic retinoids, have single-agent preclinical anticancer activity in colorectal carcinoma. Here, isobologram analysis revealed that they have synergistic cytotoxicity with retinoic acid receptor (RAR) isoform-selective agonistic retinoids such as AC261066 (RARβ2-selective agonist) and CD437 (RARγ-selective agonist) in Caco-2 cells. This synergism was confirmed by calculating the combination index (lower than 1) and the dose reduction index (higher than 1). Flow cytometry of combinatorial IC50 (the concentration causing 50% cell death) confirmed the cell cycle arrest at the SubG0-G1 phase with potentiated apoptotic and necrotic effects. The reported synergistic anticancer activity can be attributed to their ability to reduce the expression of ATP-binding cassette (ABC) transporters including P-glycoprotein (P-gp1), breast cancer resistance protein (BCRP) and multi-drug resistance-associated protein-1 (MRP1) and Heat Shock Protein 70 (Hsp70). This adds up to the apoptosis-promoting activity of EC19 and EC23, as shown by the increased Caspase-3/7 activities and DNA fragmentation leading to DNA double-strand breaks. This study sheds the light on the possible use of EC-synthetic retinoids in the rescue of multi-drug resistance in colorectal cancer using Caco-2 as a model and suggests new promising combinations between different synthetic retinoids. The current in vitro results pave the way for future studies on these compounds as possible cures for colorectal carcinoma.
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Affiliation(s)
- Mohamed R. Abdelaal
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy, Helwan University, Cairo 11795, Egypt
- Center of Scientific Excellence “Helwan Structural Biology Research, (HSBR)”, Helwan University, Cairo 11795, Egypt
| | - Esraa Ibrahim
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy, Helwan University, Cairo 11795, Egypt
- Center of Scientific Excellence “Helwan Structural Biology Research, (HSBR)”, Helwan University, Cairo 11795, Egypt
| | - Mohamed R. Elnagar
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Al-Azhar University, Cairo 11823, Egypt
| | - Sameh H. Soror
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy, Helwan University, Cairo 11795, Egypt
- Center of Scientific Excellence “Helwan Structural Biology Research, (HSBR)”, Helwan University, Cairo 11795, Egypt
| | - Hesham Haffez
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy, Helwan University, Cairo 11795, Egypt
- Center of Scientific Excellence “Helwan Structural Biology Research, (HSBR)”, Helwan University, Cairo 11795, Egypt
- Correspondence: ; Tel.: +20-1094-970-173
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2
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Abo-Elmagd I, Mahmoud AM, Al-Ghobashy MA, Nebsen M, El Sayed NS, Nofal S, Soror SH, Todd R, Elgebaly SA. Impedimetric Sensors for Cyclocreatine Phosphate Determination in Plasma Based on Electropolymerized Poly( o-phenylenediamine) Molecularly Imprinted Polymers. ACS Omega 2021; 6:31282-31291. [PMID: 34841172 PMCID: PMC8613875 DOI: 10.1021/acsomega.1c05098] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
Cyclocreatine and its water-soluble derivative, cyclocreatine phosphate (CCrP), are potent cardioprotective drugs. Based on recent animal studies, CCrP, FDA-awarded Orphan Drug Designation, has a promising role in increasing the success rate of patients undergoing heart transplantation surgery by preserving donor hearts during transportation and improving the recovery of transplanted hearts in recipient patients. In addition, CCrP is under investigation as a promising treatment for creatine transporter deficiency, an X-linked inborn error resulting in a poor quality of life for both the patients and the caregiver. A newly designed molecularly imprinted polymer (MIP) material was fabricated by the anodic electropolymerization of o-phenylenediamine on screen-printed carbon electrodes and was successfully applied as an impedimetric sensor for CCrP determination to dramatically reduce the analysis time during both the clinical trial phases and drug development process. To enhance the overall performance of the proposed sensor, studies were performed to optimize the electropolymerization conditions, incubation time, and pH of the background electrolyte. Scanning electron microscopy, electrochemical impedance spectroscopy, and cyclic voltammetry were used to characterize the behavior of the developed ultrathin MIP membrane. The CCrP-imprinted polymer has a high recognition affinity for the template molecule because of the formation of 3D complementary cavities within the polymer. The developed MIP impedimetric sensor had good linearity, repeatability, reproducibility, and stability within the linear concentration range of 1 × 10-9 to 1 × 10-7 mol/L, with a low limit of detection down to 2.47 × 10-10 mol/L. To verify the applicability of the proposed sensor, it was used to quantify CCrP in spiked plasma samples.
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Affiliation(s)
- Ibrahim
F. Abo-Elmagd
- Bioanalysis
Research Group, School of Pharmacy, Newgiza
University, Giza 12256, Egypt
| | - Amr M. Mahmoud
- Analytical
Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Medhat A. Al-Ghobashy
- Bioanalysis
Research Group, School of Pharmacy, Newgiza
University, Giza 12256, Egypt
- Analytical
Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
- Central
Administration for Drug Control, Egyptian
Drug Authority (EDA), Cairo 12654, Egypt
| | - Marianne Nebsen
- Analytical
Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Nesrine S. El Sayed
- Department
of Pharmacology and Toxicology, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Shahira Nofal
- Department
of Pharmacology and Toxicology, Faculty of Pharmacy, Helwan University, Ain Helwan, Helwan, Cairo 11795, Egypt
| | - Sameh H. Soror
- Department
of Biochemistry and Molecular Biology, Faculty of Pharmacy, Helwan University, Ain Helwan, Helwan, Cairo 11795, Egypt
- Center
for Scientific Excellence, Helwan Structural Biology Research (HSBR),
Faculty of Pharmacy, Helwan University, Ain Helwan, Helwan, Cairo 11795, Egypt
| | - Robert Todd
- ProChem
International, LLC, Sheboygan, Wisconsin 53085-3325, United States
| | - Salwa A. Elgebaly
- Nour
Heart, Inc., Vienna, Virginia 22180, United
States
- Faculty
of Medicine, University of Connecticut, Farmington, Connecticut 06030, United States
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3
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Abdelaal MR, Soror SH, Elnagar MR, Haffez H. Revealing the Potential Application of EC-Synthetic Retinoid Analogues in Anticancer Therapy. Molecules 2021; 26:molecules26020506. [PMID: 33477997 PMCID: PMC7835894 DOI: 10.3390/molecules26020506] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 12/31/2020] [Accepted: 01/08/2021] [Indexed: 12/12/2022] Open
Abstract
(1) Background and Aim: All-trans retinoic acid (ATRA) induces differentiation and inhibits growth of many cancer cells. However, resistance develops rapidly prompting the urgent need for new synthetic and potent derivatives. EC19 and EC23 are two synthetic retinoids with potent stem cell neuro-differentiation activity. Here, these compounds were screened for their in vitro antiproliferative and cytotoxic activity using an array of different cancer cell lines. (2) Methods: MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay, AV/PI (annexin V-fluorescein isothiocyanate (FITC)/propidium iodide (PI)), cell cycle analysis, immunocytochemistry, gene expression analysis, Western blotting, measurement of glutamate and total antioxidant concentrations were recruited. (3) Results: HepG2, Caco-2, and MCF-7 were the most sensitive cell lines; HepG2 (ATRA; 36.2, EC19; 42.2 and EC23; 0.74 µM), Caco-2 (ATRA; 58.0, EC19; 10.8 and EC23; 14.7 µM) and MCF-7 (ATRA; 99.0, EC19; 9.4 and EC23; 5.56 µM). Caco-2 cells were selected for further biochemical investigations. Isobologram analysis revealed the combined synergistic effects with 5-fluorouracil with substantial reduction in IC50. All retinoids induced apoptosis but EC19 had higher potency, with significant cell cycle arrest at subG0-G1, -S and G2/M phases, than ATRA and EC23. Moreover, EC19 reduced cellular metastasis in a transwell invasion assay due to overexpression of E-cadherin, retinoic acid-induced 2 (RAI2) and Werner (WRN) genes. (4) Conclusion: The present study suggests that EC-synthetic retinoids, particularly EC19, can be effective, alone or in combinations, for potential anticancer activity to colorectal cancer. Further in vivo studies are recommended to pave the way for clinical applications.
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Affiliation(s)
- Mohamed R. Abdelaal
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy, Helwan University, Cairo 11795, Egypt; (M.R.A.); (S.H.S.)
- Center of Scientific Excellence “Helwan Structural Biology Research, (HSBR)”, Helwan University, Cairo 11795, Egypt
| | - Sameh H. Soror
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy, Helwan University, Cairo 11795, Egypt; (M.R.A.); (S.H.S.)
- Center of Scientific Excellence “Helwan Structural Biology Research, (HSBR)”, Helwan University, Cairo 11795, Egypt
| | - Mohamed R. Elnagar
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Al-Azhar University, Cairo 11823, Egypt;
| | - Hesham Haffez
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy, Helwan University, Cairo 11795, Egypt; (M.R.A.); (S.H.S.)
- Center of Scientific Excellence “Helwan Structural Biology Research, (HSBR)”, Helwan University, Cairo 11795, Egypt
- Correspondence: ; Tel.: +20-1094970173
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Mangoud NOM, Ali SA, El Kassas M, Soror SH. Chitinase 3-like-1, Tolloid-like protein 1, and intergenic gene polymorphisms are predictors for hepatocellular carcinoma development after hepatitis C virus eradication by direct-acting antivirals. IUBMB Life 2021; 73:474-482. [PMID: 33347699 DOI: 10.1002/iub.2444] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 12/19/2020] [Accepted: 12/20/2020] [Indexed: 02/02/2023]
Abstract
Hepatocellular carcinoma (HCC) is a major cause of cancer death in Egypt. There is still a risk for HCC development even after eradicating hepatitis C virus (HCV) by direct-acting antivirals (DAAs). Chitinase-3-like-protein-1 (CHI3L1), a biomarker for predicting many diseases, plays an essential role in inflammation, angiogenesis, and antiapoptosis. Tolloid-like protein 1 (TLL1) may be involved in hepatic fibrogenesis and carcinogenesis. This study aimed to determine the role and combined effect of CHI3L1 (rs880633), TLL1 (rs1503298), and an intergenic (rs597533) polymorphisms on the risk of developing HCC in Egyptian patients after achieving sustained virological response (SVR) by DAAs. Blood samples were collected from 68 HCC patients, 77 non-HCC subjects, and 80 healthy controls. The DNA was extracted and analyzed for rs880633, rs1503298, and rs597533 using Genotyping TaqMan™ assay. The result of the present study showed a significant difference in genotypes and alleles frequencies in both (rs880633) and (rs597533) in HCC group as compared to healthy control and also as compared to the non-HCC group. However, regarding to (rs1503298) genotypes and alleles between the HCC and non-HCC groups, there were no significant differences. Combined polymorphism in more than one gene simultaneously showed a higher risk to HCC after SVR than an individual locus. Both allelic and genotypic variations of the CHI3L1 gene (rs880633) and an intergenic (rs597533) seemed to be significant predictors confirming a great risk for HCC susceptibility in Egyptian patients achieved SVR. Patients with a polymorphism in more than one gene showed an increased risk to HCC after SVR rather than individual locus.
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Affiliation(s)
- Nadia O M Mangoud
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy, Helwan University, Helwan, Egypt
| | - Sahar A Ali
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy, Helwan University, Helwan, Egypt
| | - Mohamed El Kassas
- Endemic Medicine Department, Faculty of Medicine, Helwan University, Helwan, Egypt
| | - Sameh H Soror
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy, Helwan University, Helwan, Egypt
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5
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Mansour SMA, Ali SA, Nofal S, Soror SH. Targeting NUPR1 for Cancer Treatment: A Risky Endeavor. Curr Cancer Drug Targets 2020; 20:768-778. [PMID: 32619170 DOI: 10.2174/1568009620666200703152523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 05/10/2020] [Accepted: 05/11/2020] [Indexed: 02/06/2023]
Abstract
NUPR1 is a transcription factor that has attracted great attention because of its various roles in cancer. Several studies were carried out to determine its molecular targets and mechanism of action to develop novel therapies against cancer. Here, we shed light on the role of NUPR1 in different types of cancer. NUPR1 regulates a complex network of pathways that may be affected by its silencing, which can cause varying effects. Its role in some types of cancer has been reported but remains incompletely understood, whereas its roles in other types of cancers have not been reported yet. Therefore, targeting NUPR1 for cancer treatment remains challenging and risky.
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Affiliation(s)
- Salma M A Mansour
- Egyptian Patent Office, Academy of Scientific Research and Technology (ASRT), 101 Kaser Al-Ainy Street, Cairo, Egypt
| | - Sahar A Ali
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Helwan University, Ain Helwan, Helwan Cairo 11795, Egypt
| | - Shaira Nofal
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Helwan University, Ain Helwan, Helwan Cairo 11795, Egypt
| | - Sameh H Soror
- Egyptian Patent Office, Academy of Scientific Research and Technology (ASRT), 101 Kaser Al-Ainy Street, Cairo, Egypt.,Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Helwan University, Ain Helwan, Helwan Cairo 11795, Egypt
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6
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Mosaab A, El-Ayadi M, Khorshed EN, Amer N, Refaat A, El-Beltagy M, Hassan Z, Soror SH, Zaghloul MS, El-Naggar S. Histone H3K27M Mutation Overrides Histological Grading in Pediatric Gliomas. Sci Rep 2020; 10:8368. [PMID: 32433577 PMCID: PMC7239884 DOI: 10.1038/s41598-020-65272-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 04/29/2020] [Indexed: 11/25/2022] Open
Abstract
Pediatric high-grade gliomas (HGG) are rare aggressive tumors that present a prognostic and therapeutic challenge. Diffuse midline glioma, H3K27M-mutant is a new entity introduced to HGG in the latest WHO classification. In this study we evaluated the presence of H3K27M mutation in 105 tumor samples histologically classified into low-grade gliomas (LGG) (n = 45), and HGG (n = 60). Samples were screened for the mutation in histone H3.3 and H3.1 variants to examine its prevalence, prognostic impact, and assess its potential clinical value in limited resource settings. H3K27M mutation was detected in 28 of 105 (26.7%) samples, and its distribution was significantly associated with midline locations (p-value < 0.0001) and HGG (p-value = 0.003). Overall and event- free survival (OS and EFS, respectively) of patients with mutant tumors did not differ significantly, neither according to histologic grade (OS p-value = 0.736, EFS p-value = 0.75) nor across anatomical sites (OS p-value = 0.068, EFS p-value = 0.153). Detection of H3K27M mutation in pediatric gliomas provides more precise risk stratification compared to traditional histopathological techniques. Hence, mutation detection should be pursued in all pediatric gliomas. Meanwhile, focusing on midline LGG can be an alternative in lower-middle-income countries to maximally optimize patients' treatment options.
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Affiliation(s)
- Amal Mosaab
- Children's Cancer Hospital Egypt 57357, Tumor Biology Research Program, Research Department, Cairo, Egypt
| | - Moatasem El-Ayadi
- Children's Cancer Hospital Egypt 57357, Department of Pediatric Oncology, Cairo, Egypt
- National Cancer Institute, Cairo University, Department of Pediatric Oncology, Cairo, Egypt
| | - Eman N Khorshed
- Children's Cancer Hospital Egypt 57357, Department of Surgical Pathology, Cairo, Egypt
- National Cancer Institute, Cairo University, Department of Surgical Pathology, Cairo, Egypt
| | - Nada Amer
- Children's Cancer Hospital Egypt 57357, Tumor Biology Research Program, Research Department, Cairo, Egypt
| | - Amal Refaat
- Children's Cancer Hospital Egypt 57357, Department of Radiology, Cairo, Egypt
- National Cancer Institute, Cairo University, Department of Radiology, Cairo, Egypt
| | - Mohamed El-Beltagy
- Children's Cancer Hospital Egypt 57357, Department of Neurosurgery, Cairo, Egypt
- Faculty of Medicine, Cairo University, Department of Neurosurgery, Cairo, Egypt
| | - Zeinab Hassan
- Faculty of Pharmacy, Helwan University, Department of Biochemistry and Molecular Biology, Cairo, Egypt
| | - Sameh H Soror
- Faculty of Pharmacy, Helwan University, Department of Biochemistry and Molecular Biology, Cairo, Egypt
| | - Mohamed Saad Zaghloul
- Children's Cancer Hospital Egypt 57357, Department of Radiotherapy, Cairo, Egypt
- National Cancer Institute, Cairo University, Department of Radiotherapy, Cairo, Egypt
| | - Shahenda El-Naggar
- Children's Cancer Hospital Egypt 57357, Tumor Biology Research Program, Research Department, Cairo, Egypt.
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7
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Omar AM, Elfaky MA, Arold ST, Soror SH, Khayat MT, Asfour HZ, Bamane FH, El-Araby ME. 1 H-Imidazole-2,5-Dicarboxamides as NS4A Peptidomimetics: Identification of a New Approach to Inhibit HCV-NS3 Protease. Biomolecules 2020; 10:E479. [PMID: 32245218 PMCID: PMC7175367 DOI: 10.3390/biom10030479] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/17/2020] [Accepted: 03/18/2020] [Indexed: 12/17/2022] Open
Abstract
The nonstructural (NS) protein NS3/4A protease is a critical factor for hepatitis C virus (HCV) maturation that requires activation by NS4A. Synthetic peptide mutants of NS4A were found to inhibit NS3 function. The bridging from peptide inhibitors to heterocyclic peptidomimetics of NS4A has not been considered in the literature and, therefore, we decided to explore this strategy for developing a new class of NS3 inhibitors. In this report, a structure-based design approach was used to convert the bound form of NS4A into 1H-imidazole-2,5-dicarboxamide derivatives as first generation peptidomimetics. This scaffold mimics the buried amino acid sequence Ile-25` to Arg-28` at the core of NS4A21`-33` needed to activate the NS3 protease. Some of the synthesized compounds (Coded MOC) were able to compete with and displace NS4A21`-33` for binding to NS3. For instance, N5-(4-guanidinobutyl)-N2-(n-hexyl)-1H-imidazole-2,5-dicarboxamide (MOC-24) inhibited the binding of NS4A21`-33` with a competition half maximal inhibitory concentration (IC50) of 1.9 ± 0.12 µM in a fluorescence anisotropy assay and stabilized the denaturation of NS3 by increasing the aggregation temperature (40% compared to NS4A21`-33`). MOC-24 also inhibited NS3 protease activity in a fluorometric assay. Molecular dynamics simulations were conducted to rationalize the differences in structure-activity relationship (SAR) between the active MOC-24 and the inactive MOC-26. Our data show that MOC compounds are possibly the first examples of NS4A peptidomimetics that have demonstrated promising activities against NS3 proteins.
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Affiliation(s)
- Abdelsattar M. Omar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Alsulaymanyah, Jeddah 21589, Saudi Arabia; (A.M.O.); (M.T.K.)
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Al-Azhar University, Nasr City, Cairo 11884, Egypt
| | - Mahmoud A. Elfaky
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, Alsulaymanyah, Jeddah 21589, Saudi Arabia;
| | - Stefan T. Arold
- Computational Bioscience Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia;
| | - Sameh H. Soror
- Center for Scientific Excellence Helwan Structural Biology Research (HSBR), Faculty of Pharmacy, Helwan University, Ain Helwan, Cairo 11795, Egypt;
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Helwan University, Ain Helwan, Cairo 11795, Egypt
| | - Maan T. Khayat
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Alsulaymanyah, Jeddah 21589, Saudi Arabia; (A.M.O.); (M.T.K.)
| | - Hani Z. Asfour
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Faida H. Bamane
- Department of Biochemistry, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Moustafa E. El-Araby
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Alsulaymanyah, Jeddah 21589, Saudi Arabia; (A.M.O.); (M.T.K.)
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El-Araby ME, Omar AM, Soror SH, Arold ST, Khayat MT, Asfour HZ, Bamane F, Elfaky MA. Synthetic bulky NS4A peptide variants bind to and inhibit HCV NS3 protease. J Adv Res 2020; 24:251-259. [PMID: 32373358 PMCID: PMC7195562 DOI: 10.1016/j.jare.2020.01.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 11/03/2019] [Accepted: 01/02/2020] [Indexed: 01/21/2023] Open
Abstract
NS4A is a non-structural multi-tasking small peptide that is essential for HCV maturation and replication. The central odd-numbered hydrophobic residues of NS4A (Val-23‘ to Leu-31‘)i are essential for activating NS3 upon NS3/4A protease complex formation. This study aims to design new specific allosteric NS3/4A protease inhibitors by mutating Val-23‘, Ile-25‘, and Ile-29‘ into bulkier amino acids. Pep-15, a synthetic peptide, showed higher binding affinity towards HCV-NS3 subtype-4 than native NS4A. The Kd of Pep-15 (80.0 ± 8.0 nM) was twice as high as that of native NS4A (169 ± 37 nM). The mutant Pep-15 inhibited the catalytic activity of HCV-NS3 by forming an inactive complex. Molecular dynamics simulations suggested that a cascade of conformational changes occurred, especially in the catalytic triad arrangements, thereby inactivating NS3. A large shift in the position of Ser-139 was observed, leading to loss of critical hydrogen bonding with His-57. Even though this study is not a classic drug discovery study—nor do we propose Pep-15 as a drug candidate—it serves as a stepping stone towards developing a potent inhibitor of hitherto untargeted HCV subtypes.
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Affiliation(s)
- Moustafa E El-Araby
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Alsulaymanyah, Jeddah 21589, Saudi Arabia
| | - Abdelsattar M Omar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Alsulaymanyah, Jeddah 21589, Saudi Arabia.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Azhar University, Cairo 11884, Egypt
| | - Sameh H Soror
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Helwan University, Ain Helwan, P.O. 11795, Cairo, Egypt.,Center for Scientific Excellence Helwan Structural Biology Research (HSBR), Faculty of Pharmacy, Helwan University, Ain Helwan, P.O. 11795, Cairo, Egypt
| | - Stefan T Arold
- King Abdullah University of Science and Technology, Computational Bioscience Research Center, Division of Biological and Environmental Sciences and Engineering, Thuwal 23955-6900, Saudi Arabia
| | - Maan T Khayat
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Alsulaymanyah, Jeddah 21589, Saudi Arabia
| | - Hani Z Asfour
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Faida Bamane
- Department of Biochemistry, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mahmoud A Elfaky
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, Alsulaymanyah, Jeddah 21589, Saudi Arabia
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9
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Tanina A, Wohlkönig A, Soror SH, Flipo M, Villemagne B, Prevet H, Déprez B, Moune M, Perée H, Meyer F, Baulard AR, Willand N, Wintjens R. A comprehensive analysis of the protein-ligand interactions in crystal structures of Mycobacterium tuberculosis EthR. Biochim Biophys Acta Proteins Proteom 2018; 1867:248-258. [PMID: 30553830 DOI: 10.1016/j.bbapap.2018.12.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 11/05/2018] [Accepted: 12/10/2018] [Indexed: 10/27/2022]
Abstract
The Mycobacterium tuberculosis EthR is a member of the TetR family of repressors, controlling the expression of EthA, a mono-oxygenase responsible for the bioactivation of the prodrug ethionamide. This protein was established as a promising therapeutic target against tuberculosis, allowing, when inhibited by a drug-like molecule, to boost the action of ethionamide. Dozens of EthR crystal structures have been solved in complex with ligands. Herein, we disclose EthR structures in complex with 18 different small molecules and then performed in-depth analysis on the complete set of EthR structures that provides insights on EthR-ligand interactions. The 81 molecules solved in complex with EthR show a large diversity of chemical structures that were split up into several chemical clusters. Two of the most striking common points of EthR-ligand interactions are the quasi-omnipresence of a hydrogen bond bridging compounds with Asn179 and the high occurrence of π-π interactions involving Phe110. A systematic analysis of the protein-ligand contacts identified eight hot spot residues that defined the basic structural features governing the binding mode of small molecules to EthR. Implications for the design of new potent inhibitors are discussed.
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Affiliation(s)
- Abdalkarim Tanina
- Unité Microbiologie, Bioorganique et Macromoléculaire (CP206/04), département R3D, Faculté de Pharmacie, Université Libre de Bruxelles, B-1050 Brussels, Belgium
| | - Alexandre Wohlkönig
- Center for Structural Biology, Vlaams Instituut voor Biotechnology (VIB), B-1050 Brussels, Belgium
| | - Sameh H Soror
- Center of scientific excellence, Helwan Structural Biology Research, Faculty of Pharmacy, Helwan University, Ain helwan, 11792 Helwan, Cairo, Egypt
| | - Marion Flipo
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, F-59000 Lille, France
| | - Baptiste Villemagne
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, F-59000 Lille, France
| | - Hugues Prevet
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, F-59000 Lille, France
| | - Benoit Déprez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, F-59000 Lille, France
| | - Martin Moune
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL- Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Hélène Perée
- Unité Microbiologie, Bioorganique et Macromoléculaire (CP206/04), département R3D, Faculté de Pharmacie, Université Libre de Bruxelles, B-1050 Brussels, Belgium
| | - Franck Meyer
- Unité Microbiologie, Bioorganique et Macromoléculaire (CP206/04), département R3D, Faculté de Pharmacie, Université Libre de Bruxelles, B-1050 Brussels, Belgium
| | - Alain R Baulard
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL- Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Nicolas Willand
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, F-59000 Lille, France.
| | - René Wintjens
- Unité Microbiologie, Bioorganique et Macromoléculaire (CP206/04), département R3D, Faculté de Pharmacie, Université Libre de Bruxelles, B-1050 Brussels, Belgium.
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10
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Mohamed MS, Sayed AI, Khedr MA, Nofal S, Soror SH. Evaluation of novel pyrrolopyrimidine derivatives as antiviral against gastroenteric viral infections. Eur J Pharm Sci 2018; 127:102-114. [PMID: 30366078 DOI: 10.1016/j.ejps.2018.10.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 10/20/2018] [Accepted: 10/22/2018] [Indexed: 11/19/2022]
Abstract
Viral gastroenteritis is a major global public-health threat. All age groups are susceptible for this infection, but its most serious consequences affect children. Rotavirus, Coxsackievirus and Adenovirus are the most common viruses that cause gastroenteritis. Herein, we synthesized novel pyrrole, pyrrolo[2,3‑d]pyrimidine and pyrrolo[3,2‑e][1,2,4]triazolo[4,3‑c]pyrimidine derivatives. The non-toxic doses of these compounds were determined using BGM cell lines. We examined all the new compounds for their anti-viral activities against Rotavirus Wa strain and Coxsackievirus B4. Compounds 2a, 2d, 5a, 5c, 5d, 7b, 7j, 7n, 14b, 14c, 14e and 14f exhibited significant antiviral activity. We interpreted the action of these compounds using molecular docking against the homology models of viral polymerase enzymes of these viruses. RMSD value of 5d/Coxsackievirus was higher than the RMSD value for 5d/rotavirus and hence better as a stability parameter, which can be correlated to the biological activity.
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Affiliation(s)
- Mosaad S Mohamed
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Helwan University, Ain Helwan, Cairo, Egypt
| | - Amira I Sayed
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Helwan University, Ain Helwan, Cairo, Egypt
| | - Mohammed A Khedr
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Helwan University, Ain Helwan, Cairo, Egypt
| | - Shahira Nofal
- Department of Pharmacology and Toxicology, faculty of Pharmacy, Helwan University, Ain Helwan, Cairo, Egypt
| | - Sameh H Soror
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy, Helwan University, Ain Helwan, Cairo, Egypt; Center for scientific excellence "Helwan Structural Biology Research (HSBR)", Cairo, Egypt..
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11
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Mohamed MS, Sayed AI, Khedr MA, Soror SH. Design, synthesis, assessment, and molecular docking of novel pyrrolopyrimidine (7-deazapurine) derivatives as non-nucleoside hepatitis C virus NS5B polymerase inhibitors. Bioorg Med Chem 2016; 24:2146-57. [PMID: 27052365 DOI: 10.1016/j.bmc.2016.03.046] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 03/16/2016] [Accepted: 03/27/2016] [Indexed: 12/16/2022]
Abstract
Hepatitis C virus (HCV) infection is highly persistent and presents an unmet medical need requiring more effective treatment options. This has spurred intensive efforts to discover novel anti-HCV agents. The RNA-dependent RNA polymerase (RdRp), NS5B of HCV, constitutes a selective target for drug discovery due to its absence in human cells; also, it is the centerpiece for viral replication. Here, we synthesized novel pyrrole, pyrrolo[2,3-d]pyrimidine and pyrrolo[3,2-e][1,2,4]triazolo[4,3-c]pyrimidine derivatives. The non-toxic doses of these compounds on Huh 7.5 cell line were determined and their antiviral activity against HCVcc genotype 4a was examined. Compounds 7j, 7f, 5c, 12i and 12f showed significant anti HCV activity. The percent of reduction for the non-toxic doses of 7j, 7f, 5c, 12i and 12f were 90%, 76.7±5.8%, 73.3±5.8%, 70% and 63.3±5.8%, respectively. The activity of these compounds was interpreted by molecular docking against HCV NS5B polymerase enzyme.
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Affiliation(s)
- Mosaad S Mohamed
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Helwan University, Ain Helwan, Cairo, Egypt
| | - Amira I Sayed
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Helwan University, Ain Helwan, Cairo, Egypt
| | - Mohammed A Khedr
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Helwan University, Ain Helwan, Cairo, Egypt
| | - Sameh H Soror
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy, Helwan University, Ain Helwan, University Campus, 11795 Cairo, Egypt; Center for Scientific Excellence 'Helwan Structural Biology Research (HSBR)', Cairo, Egypt.
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12
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Mohamed MS, Abd El-Hameed RH, Sayed AI, Soror SH. Novel antiviral compounds against gastroenteric viral infections. Arch Pharm (Weinheim) 2015; 348:194-205. [PMID: 25704120 DOI: 10.1002/ardp.201400387] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Revised: 12/24/2014] [Accepted: 01/09/2015] [Indexed: 11/07/2022]
Abstract
Viral gastroenteritis is a serious viral infection which affects a large number of individuals around the world, most of them being children. The infection may occur due to different viruses, for example, coxsackievirus, adenovirus, and rotavirus. There is no available cure for such infections, and the treatment mainly depends on hospitalization and administration of nutritional supports. A new antiviral agent against gastroenteritis viral infection will be a breakthrough in healthcare. Pyrrole and pyrrolopyrimidine derivatives are well known for their biological activity as antibacterial, antifungal, and anticancer agents. These compounds also proved to possess antiviral activity. Here, we synthesized novel pyrrole and pyrrolopyrimidine compounds and examined their antiviral activity. We synthesized several new pyrrole, pyrrolo[2,3-d]pyrimidine, and pyrrolo[3,2-e][1,2,4]triazolo[1,5-c]pyrimidine derivatives. The characterization of all synthesized compounds was based on microanalysis and spectral data. Moreover, we determined the non-toxic doses of these compounds on BGM, Hep-2, and MA-104 cells. We tested all the synthesized compounds for their antiviral activities against coxsackievirus B4, adenovirus type 7, and rotavirus Wa strain. Several compounds exhibited significant activities as antiviral agents.
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Affiliation(s)
- Mosaad S Mohamed
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Helwan University, Ain Helwan, Helwan, Egypt
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13
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Villemagne B, Flipo M, Blondiaux N, Crauste C, Malaquin S, Leroux F, Piveteau C, Villeret V, Brodin P, Villoutreix BO, Sperandio O, Soror SH, Wohlkönig A, Wintjens R, Deprez B, Baulard AR, Willand N. Ligand efficiency driven design of new inhibitors of Mycobacterium tuberculosis transcriptional repressor EthR using fragment growing, merging, and linking approaches. J Med Chem 2014; 57:4876-88. [PMID: 24818704 DOI: 10.1021/jm500422b] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tuberculosis remains a major cause of mortality and morbidity, killing each year more than one million people. Although the combined use of first line antibiotics (isoniazid, rifampicin, pyrazinamide, and ethambutol) is efficient to treat most patients, the rapid emergence of multidrug resistant strains of Mycobacterium tuberculosis stresses the need for alternative therapies. Mycobacterial transcriptional repressor EthR is a key player in the control of second-line drugs bioactivation such as ethionamide and has been shown to impair the sensitivity of the human pathogen Mycobacterium tuberculosis to this antibiotic. As a way to identify new potent ligands of this protein, we have developed fragment-based approaches. In the current study, we combined surface plasmon resonance assay, X-ray crystallography, and ligand efficiency driven design for the rapid discovery and optimization of new chemotypes of EthR ligands starting from a fragment. The design, synthesis, and in vitro and ex vivo activities of these compounds will be discussed.
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14
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Abskharon RNN, Giachin G, Wohlkonig A, Soror SH, Pardon E, Legname G, Steyaert J. Probing the N-terminal β-sheet conversion in the crystal structure of the human prion protein bound to a nanobody. J Am Chem Soc 2014; 136:937-44. [PMID: 24400836 DOI: 10.1021/ja407527p] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Prions are fatal neurodegenerative transmissible agents causing several incurable illnesses in humans and animals. Prion diseases are caused by the structural conversion of the cellular prion protein, PrP(C), into its misfolded oligomeric form, known as prion or PrP(Sc). The canonical human PrP(C) (HuPrP) fold features an unstructured N-terminal part (residues 23-124) and a well-defined C-terminal globular domain (residues 125-231). Compelling evidence indicates that an evolutionary N-terminal conserved motif AGAAAAGA (residues 113-120) plays an important role in the conversion to PrP(Sc). The intrinsic flexibility of the N-terminal has hampered efforts to obtain detailed atomic information on the structural features of this palindromic region. In this study, we crystallized the full-length HuPrP in complex with a nanobody (Nb484) that inhibits prion propagation. In the complex, the prion protein is unstructured from residue 23 to 116. The palindromic motif adopts a stable and fully extended configuration to form a three-stranded antiparallel β-sheet with the β1 and β2 strands, demonstrating that the full-length HuPrP(C) can adopt a more elaborate β0-β1-α1-β2-α2-α3 structural organization than the canonical β1-α1-β2-α2-α3 prion-like fold. From this structure, it appears that the palindromic motif mediates β-enrichment in the PrP(C) monomer as one of the early events in the conversion of PrP(C) into PrP(Sc).
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Affiliation(s)
- Romany N N Abskharon
- Structural Biology Brussels, Vrije Universiteit Brussel , Pleinlaan 2, 1050 Brussels, Belgium
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15
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Volkov AN, Wohlkonig A, Soror SH, van Nuland NAJ. Expression, Purification, Characterization, and Solution Nuclear Magnetic Resonance Study of Highly Deuterated Yeast Cytochrome c Peroxidase with Enhanced Solubility. Biochemistry 2013; 52:2165-75. [DOI: 10.1021/bi400220w] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexander N. Volkov
- Jean Jeener NMR Centre, Structural
Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Molecular Recognition Unit,
Department of Structural Biology, VIB,
Pleinlaan 2, 1050 Brussels, Belgium
| | - Alexandre Wohlkonig
- JAST lab, Department of Structural
Biology, VIB, Pleinlaan 2, 1050 Brussels,
Belgium
| | - Sameh H. Soror
- JAST lab, Department of Structural
Biology, VIB, Pleinlaan 2, 1050 Brussels,
Belgium
- Department of Biochemistry
and
Molecular Biology, Faculty of Pharmacy, Helwan University, Cairo, Egypt
| | - Nico A. J. van Nuland
- Jean Jeener NMR Centre, Structural
Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Molecular Recognition Unit,
Department of Structural Biology, VIB,
Pleinlaan 2, 1050 Brussels, Belgium
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16
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Abskharon RNN, Ramboarina S, El Hassan H, Gad W, Apostol MI, Giachin G, Legname G, Steyaert J, Messens J, Soror SH, Wohlkonig A. A novel expression system for production of soluble prion proteins in E. coli. Microb Cell Fact 2012; 11:6. [PMID: 22233534 PMCID: PMC3283519 DOI: 10.1186/1475-2859-11-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 01/10/2012] [Indexed: 11/16/2022] Open
Abstract
Expression of eukaryotic proteins in Escherichia coli is challenging, especially when they contain disulfide bonds. Since the discovery of the prion protein (PrP) and its role in transmissible spongiform encephalopathies, the need to obtain large quantities of the recombinant protein for research purposes has been essential. Currently, production of recombinant PrP is achieved by refolding protocols. Here, we show that the co-expression of two different PrP with the human Quiescin Sulfhydryl OXidase (QSOX), a human chaperone with thiol/disulfide oxidase activity, in the cytoplasm of E. coli produces soluble recombinant PrP. The structural integrity of the soluble PrP has been confirmed by nuclear magnetic resonance spectroscopy, demonstrating that properly folded PrP can be easily expressed in bacteria. Furthermore, the soluble recombinant PrP produced with this method can be used for functional and structural studies.
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17
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Carette X, Blondiaux N, Willery E, Hoos S, Lecat-Guillet N, Lens Z, Wohlkönig A, Wintjens R, Soror SH, Frénois F, Dirié B, Villeret V, England P, Lippens G, Deprez B, Locht C, Willand N, Baulard AR. Structural activation of the transcriptional repressor EthR from Mycobacterium tuberculosis by single amino acid change mimicking natural and synthetic ligands. Nucleic Acids Res 2011; 40:3018-30. [PMID: 22156370 PMCID: PMC3326297 DOI: 10.1093/nar/gkr1113] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Ethionamide is an antituberculous drug for the treatment of multidrug-resistant Mycobacterium tuberculosis. This antibiotic requires activation by the monooxygenase EthA to exert its activity. Production of EthA is controlled by the transcriptional repressor EthR, a member of the TetR family. The sensitivity of M. tuberculosis to ethionamide can be artificially enhanced using synthetic ligands of EthR that allosterically inactivate its DNA-binding activity. Comparison of several structures of EthR co-crystallized with various ligands suggested that the structural reorganization of EthR resulting in its inactivation is controlled by a limited portion of the ligand-binding-pocket. In silico simulation predicted that mutation G106W may mimic ligands. X-ray crystallography of variant G106W indeed revealed a protein structurally similar to ligand-bound EthR. Surface plasmon resonance experiments established that this variant is unable to bind DNA, while thermal shift studies demonstrated that mutation G106W stabilizes EthR as strongly as ligands. Proton NMR of the methyl regions showed a lesser contribution of exchange broadening upon ligand binding, and the same quenched dynamics was observed in apo-variant G106W. Altogether, we here show that the area surrounding Gly106 constitutes the molecular switch involved in the conformational reorganization of EthR. These results also shed light on the mechanistic of ligand-induced allosterism controlling the DNA binding properties of TetR family repressors.
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Affiliation(s)
- Xavier Carette
- Center for Infection and Immunity of Lille, F-59019 Lille, France
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18
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Flipo M, Desroses M, Lecat-Guillet N, Villemagne B, Blondiaux N, Leroux F, Piveteau C, Mathys V, Flament MP, Siepmann J, Villeret V, Wohlkönig A, Wintjens R, Soror SH, Christophe T, Jeon HK, Locht C, Brodin P, Déprez B, Baulard AR, Willand N. Ethionamide boosters. 2. Combining bioisosteric replacement and structure-based drug design to solve pharmacokinetic issues in a series of potent 1,2,4-oxadiazole EthR inhibitors. J Med Chem 2011; 55:68-83. [PMID: 22098589 DOI: 10.1021/jm200825u] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mycobacterial transcriptional repressor EthR controls the expression of EthA, the bacterial monooxygenase activating ethionamide, and is thus largely responsible for the low sensitivity of the human pathogen Mycobacterium tuberculosis to this antibiotic. We recently reported structure-activity relationships of a series of 1,2,4-oxadiazole EthR inhibitors leading to the discovery of potent ethionamide boosters. Despite high metabolic stability, pharmacokinetic evaluation revealed poor mice exposure; therefore, a second phase of optimization was required. Herein a structure-property relationship study is reported according to the replacement of the two aromatic heterocycles: 2-thienyl and 1,2,4-oxadiazolyl moieties. This work was done using a combination of structure-based drug design and in vitro/ex vivo evaluations of ethionamide boosters on the targeted protein EthR and on the human pathogen Mycobacterium tuberculosis. Thanks to this process, we identified compound 42 (BDM41906), which displays improved efficacy in addition to high exposure to mice after oral administration.
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Affiliation(s)
- Marion Flipo
- Université Lille Nord de France, F-59000 Lille, France
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19
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Van de Water K, Soror SH, Wohlkonig A, van Nuland NAJ, Volkov AN. Crystallization and preliminary X-ray diffraction analysis of kanamycin-binding β-lactamase in complex with its ligand. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:703-6. [PMID: 21636917 DOI: 10.1107/s1744309111013832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 04/12/2011] [Indexed: 11/10/2022]
Abstract
TEM-1 β-lactamase is a highly efficient enzyme that is involved in bacterial resistance against β-lactam antibiotics such as penicillin. It is also a robust scaffold protein which can be engineered by molecular-evolution techniques to bind a variety of targets. One such β-lactamase variant (BlaKr) has been constructed to bind kanamycin (kan) and other aminoglycoside antibiotics, which are neither substrates nor ligands of native β-lactamases. In addition to recognizing kan, BlaKr activity is up-regulated by its binding via an activation mechanism which is not yet understood at the molecular level. In order to fill this gap, determination of the structure of the BlaKr-kan complex was embarked upon. A crystallization condition for BlaKr-kan was identified using high-throughput screening, and crystal growth was further optimized using streak-seeding and hanging-drop methods. The crystals belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 47.01, b = 72.33, c = 74.62 Å, and diffracted to 1.67 Å resolution using synchrotron radiation. The X-ray structure of BlaKr with its ligand kanamycin should provide the molecular-level details necessary for understanding the activation mechanism of the engineered enzyme.
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Affiliation(s)
- Karen Van de Water
- Department of Molecular and Cellular Interactions, Vrije Universiteit Brussel, Pleinlaan 2, Brussels, Belgium
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20
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Abskharon RNN, Soror SH, Pardon E, El Hassan H, Legname G, Steyaert J, Wohlkonig A. Combining in-situ proteolysis and microseed matrix screening to promote crystallization of PrPc-nanobody complexes. Protein Eng Des Sel 2011; 24:737-41. [PMID: 21536542 DOI: 10.1093/protein/gzr017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Prion proteins (PrPs) are difficult to crystallize, probably due to their inherent flexibility. Several PrPs structures have been solved by nuclear magnetic resonance (NMR) techniques; however, only three structures were solved by X-ray crystallography. Here we combined in-situ proteolysis with automated microseed matrix screening (MMS) to crystallize two different PrP(C)-nanobody (Nb) complexes. Nanobodies are single-domain antibodies derived from heavy-chain-only antibodies of camelids. Initial crystallization screening conditions using in-situ proteolysis of mouse prion (23-230) in complex with a nanobody (Nb_PrP_01) gave thin needle aggregates, which were of poor diffraction quality. Next, we used these microcrystals as nucleants for automated MMS. Good-quality crystals were obtained from mouse PrP (89-230)/Nb_PrP_01, belonged to the monoclinic space group P 1 21 1, with unit-cell parameters a = 59.13, b = 63.80, c = 69.79 Å, β = 101.96° and diffracted to 2.1 Å resolution using synchrotron radiation. Human PrP (90-231)/Nb_PrP_01 crystals belonged to the monoclinic space group C2, with unit-cell parameters a = 131.86, b = 45.78, c = 45.09 Å, β = 96.23° and diffracted to 1.5 Å resolution. This combined strategy benefits from the power of the MMS technique without suffering from the drawbacks of the in-situ proteolysis. It proved to be a successful strategy to crystallize PrP-nanobodies complexes and could be exploited for the crystallization of other difficult antigen-antibody complexes.
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21
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Abskharon RNN, Soror SH, Pardon E, El Hassan H, Legname G, Steyaert J, Wohlkonig A. Crystallization and preliminary X-ray diffraction analysis of a specific VHH domain against mouse prion protein. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1644-6. [PMID: 21139215 DOI: 10.1107/s1744309110042168] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Accepted: 10/17/2010] [Indexed: 11/10/2022]
Abstract
Prion disorders are infectious diseases that are characterized by the conversion of the cellular prion protein PrPC into the pathogenic isoform PrPSc. Specific antibodies that interact with the cellular prion protein have been shown to inhibit this transition. Recombinant VHHs (variable domain of dromedary heavy-chain antibodies) or nanobodies are single-domain antibodies, making them the smallest antigen-binding fragments. A specific nanobody (Nb_PrP_01) was raised against mouse PrPC. A crystallization condition for this recombinant nanobody was identified using high-throughput screening. The crystals were optimized using streak-seeding and the hanging-drop method. The crystals belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a=30.04, b=37.15, c=83.00 Å, and diffracted to 1.23 Å resolution using synchrotron radiation. The crystal structure of this specific nanobody against PrPC together with the known PrPC structure may help in understanding the PrPC/PrPSc transition mechanism.
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Affiliation(s)
- Romany N N Abskharon
- Structural Biology Brussels, Free University of Brussels, Pleinlaan 2, Brussels 1050, Belgium
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22
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Soror SH, Rao R, Cullum J. Mining the genome sequence for novel enzyme activity: characterisation of an unusual member of the hormone-sensitive lipase family of esterases from the genome of Streptomyces coelicolor A3 (2). Protein Eng Des Sel 2009; 22:333-9. [DOI: 10.1093/protein/gzp009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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23
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Soror SH, Verma V, Rao R, Rasool S, Koul S, Qazi GN, Cullum J. A cold-active esterase of Streptomyces coelicolor A3(2): from genome sequence to enzyme activity. J Ind Microbiol Biotechnol 2008; 34:525-31. [PMID: 17554575 DOI: 10.1007/s10295-007-0224-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2006] [Accepted: 05/04/2007] [Indexed: 11/29/2022]
Abstract
The genome sequence of Streptomyces coelicolor A3(2) contains 51 putative lipase and esterase genes mostly of unknown function. The gene estB (locus SCO 6966) was expressed as a His-tagged protein in E. coli. Esterase B was active at low temperatures exerting its maximum activity at 30 degrees C and retaining more than 25% of its activity at 4 degrees C. The optimum pH was 8-8.5. The enzyme was active against short synthetic p-nitrophenylesters (C2-C10) with maximum activity towards the acetate ester (C2). The esterase was tested on 13 series of racemic esters of potential interest for the synthesis of chiral pharmaceutical compounds. 4 of the series were substrates and a modest degree of enantioselectivity was observed (enantiomeric ratios of 1.1-1.9).
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Affiliation(s)
- Sameh H Soror
- LB Genetik University of Kaiserslautern, Postfach 3049, 67653 Kaiserslautern, Germany
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